Tomography Short Course 20212021-02-10T20:36:36+00:00


  • 3 days.

  • 1 day of lectures and roundtables.

  • 2 days of hands-on practicals.

  • April 12-14, 2021.

  • At no cost.

  • Virtual workshop

This workshop will be held remotely, registration is required, and all times are EST.

Questions? Email nccatinfo [at]


NCCAT Tomography Shortcourse

April 12-14, 2021

SEMC and NCCAT will be offering a 3-day workshop focused on the theory and practice of tomographic methods. Cryoelectron tomography (cryoET) is a powerful new method for directly visualizing macromolecular associations and organization in native cells Traditionally, macromolecular structure determination has been limited to the analysis of isolated molecules and structures. CryoET has the unique ability to visualize macromolecular organization in native cells; it utilizes the intrinsic contrast of frozen cellular material to directly image macromolecules.

Short-course Agenda

April 12, 2021
Day 1: Lectures and Roundtables

12:00-12:05 Welcome
12:05-12:50 Lecture 1 – Intro and overview of ET
Wei Dai (Rutgers University)
12:50-13:35 Lecture 2 – FIB-SEM
Bill Rice (New York University)
13:35-14:20 Roundtable 1 – Making windows into cells & Choosing the right in situ target and model system
14:20-14:45 Break
14:45-15:30 Lecture 3 – Cryo-Applications and sub-tomogram averaging
Alex Noble (NYSBC/SEMC)
15:30-16:15 Lecture 4 – Automated reconstruction, subtomogram averaging methods & data interpretation
Steven Ludtke (Baylor College of Medicine)
16:15-17:00 Roundtable 2 – The future of in situ cellular structural biology
17:00-17:30 Closing and networking/break out rooms

April 13, 2021
Day 2: Practical – Appion Protomo (
limited space available)

12:00-12:05 Welcome
12:05-13:00 Roundtable 3 – Introductions and flash talks by short course attendees
13:00-17:00 Practical 1
Appion III : Fiducial-less Tomography Practical
Alex Noble (NYSBC/SEMC)
13:00-13:30 Full Overview – Tilt-Series Collection, Appion-Protomo alignment, and Sub-tomogram Processing
13:30-14:00 In-Depth Appion-Protomo Workflow
14:00-14:30 Q&A and Practice!
14:30-15:00 Discussion/Break
15:00-15:10 Overview – Sub-Tomogram Alignment and Dynamo
15:10-15:35 Particle Picking using a Template
15:35-16:00 Membrane, and Filament Picking
16:00-16:30 Sub-Tomogram Alignment, Classification, and tools to transfer to Warp/M/Relion
16:30-17:00 Q&A and Practice!
17:00 End

April 14, 2021
Day 3: Practical – EMAN2
(limited space available)

12:00-12:05 Welcome
12:05-16:45 Practical 2
EMAN2 tools, sub-tomogram averaging and annotation
Muyuan Chen (Baylor College of Medicine)
12:05-12:50 Basic user interface and visualization of raw data.
12:50-13:35 Tilt series alignment, tomogram reconstruction and CTF estimation
13:35-14:30 Methods for picking particles from tomograms
14:30-15:00 Break
15:00-16:15 Generating initial model and setting up subtomogram averaging runs
16:15-16:45 Q&A
16:45-17:00 Closing & Wrap up

*All times EST.


Rutgers University

Wei Dai

Baylor College of Medicine

Steven Ludtke

New York University

William Rice

New York Structural Biology Center

Alex Noble

Baylor College of Medicine

Muyuan Chen